Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R88L8

Calculation Name: 4U0Q-B-Xray372

Preferred Name: Basigin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4U0Q

Chain ID: B

ChEMBL ID: CHEMBL3580492

UniProt ID: P35613

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1588890.548033
FMO2-HF: Nuclear repulsion 1518210.655463
FMO2-HF: Total energy -70679.89257
FMO2-MP2: Total energy -70882.728597


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:23:ALA)


Summations of interaction energy for fragment #1(B:23:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-3.808-1.161-0.015-1.418-1.2150.005
Interaction energy analysis for fragmet #1(B:23:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.002
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B25THR0-0.041-0.0303.831-1.2580.912-0.019-1.306-0.8450.005
4B26VAL0-0.011-0.0016.5840.2680.2680.0000.0000.0000.000
5B27PHE0-0.028-0.0138.8280.0710.0710.0000.0000.0000.000
6B28THR00.0550.01912.4320.0940.0940.0000.0000.0000.000
7B29THR0-0.075-0.04514.944-0.013-0.0130.0000.0000.0000.000
8B30VAL00.0110.01618.7170.0210.0210.0000.0000.0000.000
9B31GLU-1-0.891-0.94121.935-0.179-0.1790.0000.0000.0000.000
10B32ASP-1-0.856-0.92825.002-0.082-0.0820.0000.0000.0000.000
11B33LEU0-0.059-0.04226.876-0.001-0.0010.0000.0000.0000.000
12B34GLY0-0.036-0.00630.5670.0070.0070.0000.0000.0000.000
13B35SER0-0.027-0.00433.597-0.001-0.0010.0000.0000.0000.000
14B36LYS10.8130.88729.4790.0320.0320.0000.0000.0000.000
15B37ILE00.0450.03124.772-0.006-0.0060.0000.0000.0000.000
16B38LEU0-0.056-0.02122.6130.0150.0150.0000.0000.0000.000
17B39LEU0-0.0220.00819.326-0.019-0.0190.0000.0000.0000.000
18B40THR0-0.008-0.03217.0080.0210.0210.0000.0000.0000.000
19B41CYS0-0.109-0.03712.556-0.023-0.0230.0000.0000.0000.000
20B42SER00.0190.00712.7800.0940.0940.0000.0000.0000.000
21B43LEU0-0.056-0.0105.191-0.150-0.1500.0000.0000.0000.000
22B44ASN00.001-0.0038.3160.2490.2490.0000.0000.0000.000
23B45ASP-1-0.862-0.9516.597-2.269-2.2690.0000.0000.0000.000
24B46SER0-0.029-0.0023.584-1.032-0.9320.006-0.060-0.0460.000
25B47ALA0-0.001-0.0083.8230.2160.4120.000-0.029-0.1670.000
26B48THR0-0.029-0.0124.7420.0640.134-0.001-0.004-0.0650.000
27B49GLU-1-0.817-0.9147.139-0.187-0.1870.0000.0000.0000.000
28B50VAL0-0.081-0.0439.4530.1240.1240.0000.0000.0000.000
29B51THR0-0.079-0.04011.364-0.028-0.0280.0000.0000.0000.000
30B52GLY00.0510.02213.957-0.044-0.0440.0000.0000.0000.000
31B53HIS10.7650.86713.333-0.007-0.0070.0000.0000.0000.000
32B54ARG10.7940.86814.721-0.270-0.2700.0000.0000.0000.000
33B55TRP00.0530.03215.666-0.018-0.0180.0000.0000.0000.000
34B56LEU0-0.063-0.04115.9520.0250.0250.0000.0000.0000.000
35B57LYS10.8860.95519.3700.0020.0020.0000.0000.0000.000
36B58GLY00.0070.00521.636-0.005-0.0050.0000.0000.0000.000
37B59GLY0-0.0210.00922.1400.0170.0170.0000.0000.0000.000
38B60VAL0-0.020-0.03219.889-0.004-0.0040.0000.0000.0000.000
39B61VAL0-0.0040.00621.420-0.002-0.0020.0000.0000.0000.000
40B62LEU00.0110.00921.022-0.006-0.0060.0000.0000.0000.000
41B63LYS10.8240.88518.768-0.154-0.1540.0000.0000.0000.000
42B64GLU-1-0.832-0.89718.2280.0500.0500.0000.0000.0000.000
43B65ASP-1-0.801-0.89717.8610.1980.1980.0000.0000.0000.000
44B66ALA0-0.0010.00518.3350.0200.0200.0000.0000.0000.000
45B67LEU0-0.030-0.01318.939-0.012-0.0120.0000.0000.0000.000
46B68PRO00.0490.04315.3790.0080.0080.0000.0000.0000.000
47B69GLY00.0220.00414.693-0.028-0.0280.0000.0000.0000.000
48B70GLN00.0170.00010.5360.0140.0140.0000.0000.0000.000
49B71LYS10.8510.92212.3710.1250.1250.0000.0000.0000.000
50B72THR0-0.021-0.00414.2180.0510.0510.0000.0000.0000.000
51B73GLU-1-0.821-0.89916.801-0.154-0.1540.0000.0000.0000.000
52B74PHE00.014-0.00219.9500.0270.0270.0000.0000.0000.000
53B75LYS10.9520.98521.9120.0410.0410.0000.0000.0000.000
54B76VAL00.0010.00723.8410.0100.0100.0000.0000.0000.000
55B77ASP-1-0.765-0.87826.712-0.035-0.0350.0000.0000.0000.000
56B78SER00.044-0.00229.941-0.002-0.0020.0000.0000.0000.000
57B79ASP-1-0.911-0.94331.835-0.029-0.0290.0000.0000.0000.000
58B80ASP-1-0.834-0.91727.641-0.011-0.0110.0000.0000.0000.000
59B81GLN0-0.103-0.02927.008-0.006-0.0060.0000.0000.0000.000
60B82TRP0-0.113-0.07526.728-0.006-0.0060.0000.0000.0000.000
61B83GLY00.0190.01224.5370.0090.0090.0000.0000.0000.000
62B84GLU-1-0.867-0.92017.802-0.093-0.0930.0000.0000.0000.000
63B85TYR0-0.007-0.01219.1470.0250.0250.0000.0000.0000.000
64B86SER0-0.005-0.02114.597-0.018-0.0180.0000.0000.0000.000
65B88VAL0-0.010-0.03010.965-0.015-0.0150.0000.0000.0000.000
66B89PHE00.003-0.0058.691-0.037-0.0370.0000.0000.0000.000
67B90LEU0-0.047-0.0109.8990.1520.1520.0000.0000.0000.000
68B91PRO00.0340.0209.755-0.088-0.0880.0000.0000.0000.000
69B92GLU-1-0.787-0.8739.1430.6010.6010.0000.0000.0000.000
70B93PRO0-0.057-0.0305.8560.0160.0160.0000.0000.0000.000
71B94MET0-0.014-0.0044.8290.2270.2270.0000.0000.0000.000
72B95GLY00.0610.0304.492-0.479-0.368-0.001-0.019-0.0920.000
73B96THR0-0.064-0.0346.1640.1280.1280.0000.0000.0000.000
74B97ALA00.0080.0148.391-0.140-0.1400.0000.0000.0000.000
75B98ASN00.004-0.00311.1760.0740.0740.0000.0000.0000.000
76B99ILE00.0030.00214.718-0.039-0.0390.0000.0000.0000.000
77B100GLN0-0.055-0.03417.6870.0360.0360.0000.0000.0000.000
78B101LEU00.0000.01420.468-0.013-0.0130.0000.0000.0000.000
79B102HIS00.0580.01223.5780.0150.0150.0000.0000.0000.000
80B103GLY00.0340.01226.0100.0020.0020.0000.0000.0000.000
81B104PRO00.0170.01828.622-0.004-0.0040.0000.0000.0000.000
82B105PRO0-0.068-0.02431.6840.0010.0010.0000.0000.0000.000
83B106ARG10.8660.91532.9490.0170.0170.0000.0000.0000.000
84B107VAL0-0.077-0.01935.060-0.002-0.0020.0000.0000.0000.000
85B108LYS10.9680.98037.2650.0010.0010.0000.0000.0000.000
86B109ALA00.0450.02340.324-0.002-0.0020.0000.0000.0000.000
87B110VAL0-0.079-0.02841.9600.0020.0020.0000.0000.0000.000
88B111LYS10.8560.90843.5150.0020.0020.0000.0000.0000.000
89B112SER00.0580.02845.529-0.001-0.0010.0000.0000.0000.000
90B113SER0-0.050-0.01447.7360.0000.0000.0000.0000.0000.000
91B114GLU-1-0.798-0.88451.086-0.002-0.0020.0000.0000.0000.000
92B115HIS0-0.020-0.02253.5470.0000.0000.0000.0000.0000.000
93B116ILE00.0140.02654.3870.0010.0010.0000.0000.0000.000
94B117ASN00.001-0.02058.6470.0010.0010.0000.0000.0000.000
95B118GLU-1-0.800-0.85662.086-0.004-0.0040.0000.0000.0000.000
96B119GLY0-0.054-0.02364.5390.0000.0000.0000.0000.0000.000
97B120GLU-1-0.882-0.93160.242-0.005-0.0050.0000.0000.0000.000
98B121THR0-0.001-0.01156.2740.0000.0000.0000.0000.0000.000
99B122ALA0-0.037-0.00955.4010.0010.0010.0000.0000.0000.000
100B123MET00.0070.00248.816-0.002-0.0020.0000.0000.0000.000
101B124LEU0-0.0260.00149.7950.0010.0010.0000.0000.0000.000
102B125VAL00.0130.00643.693-0.002-0.0020.0000.0000.0000.000
103B126CYS0-0.093-0.02142.7470.0020.0020.0000.0000.0000.000
104B127LYS10.9010.93936.4390.0120.0120.0000.0000.0000.000
105B128SER0-0.032-0.05735.5320.0010.0010.0000.0000.0000.000
106B129GLU-1-0.791-0.87331.161-0.017-0.0170.0000.0000.0000.000
107B130SER0-0.0050.01730.496-0.001-0.0010.0000.0000.0000.000
108B131VAL00.0270.02126.491-0.003-0.0030.0000.0000.0000.000
109B132PRO00.003-0.00728.178-0.002-0.0020.0000.0000.0000.000
110B133PRO00.0020.01130.4000.0060.0060.0000.0000.0000.000
111B134VAL0-0.024-0.02033.349-0.001-0.0010.0000.0000.0000.000
112B135THR0-0.059-0.02336.674-0.001-0.0010.0000.0000.0000.000
113B136ASP-1-0.879-0.93038.756-0.044-0.0440.0000.0000.0000.000
114B137TRP0-0.035-0.03539.1270.0030.0030.0000.0000.0000.000
115B138ALA0-0.0070.00744.1510.0000.0000.0000.0000.0000.000
116B139TRP00.016-0.01346.6440.0020.0020.0000.0000.0000.000
117B140TYR00.0120.01048.231-0.001-0.0010.0000.0000.0000.000
118B141LYS10.8430.94352.3900.0080.0080.0000.0000.0000.000
119B142ILE0-0.039-0.02950.4950.0000.0000.0000.0000.0000.000
120B143THR0-0.031-0.02454.9420.0010.0010.0000.0000.0000.000
121B144ASP-1-0.959-0.97757.062-0.005-0.0050.0000.0000.0000.000
122B145SER0-0.028-0.00157.8950.0000.0000.0000.0000.0000.000
123B146GLU-1-0.929-0.97755.767-0.015-0.0150.0000.0000.0000.000
124B147ASP-1-0.798-0.86252.138-0.011-0.0110.0000.0000.0000.000
125B148LYS10.9320.97555.0930.0120.0120.0000.0000.0000.000
126B149ALA00.022-0.00853.7350.0000.0000.0000.0000.0000.000
127B150LEU0-0.056-0.01453.7310.0000.0000.0000.0000.0000.000
128B151MET00.000-0.00451.826-0.002-0.0020.0000.0000.0000.000
129B152ASN00.0320.01052.7250.0020.0020.0000.0000.0000.000
130B153GLY00.0350.01054.742-0.001-0.0010.0000.0000.0000.000
131B154SER0-0.022-0.00557.8610.0010.0010.0000.0000.0000.000
132B155GLU-1-0.864-0.96259.672-0.012-0.0120.0000.0000.0000.000
133B156SER0-0.039-0.02061.9860.0010.0010.0000.0000.0000.000
134B157ARG10.7770.87560.7610.0110.0110.0000.0000.0000.000
135B158PHE0-0.0090.01756.1560.0010.0010.0000.0000.0000.000
136B159PHE00.0140.01954.635-0.002-0.0020.0000.0000.0000.000
137B160VAL00.009-0.00948.6410.0010.0010.0000.0000.0000.000
138B161SER0-0.0250.00747.953-0.002-0.0020.0000.0000.0000.000
139B162SER00.0270.00244.0200.0020.0020.0000.0000.0000.000
140B163SER0-0.0140.00341.086-0.002-0.0020.0000.0000.0000.000
141B164GLN00.0450.00435.095-0.001-0.0010.0000.0000.0000.000
142B165GLY00.0220.02236.5140.0010.0010.0000.0000.0000.000
143B166ARG10.8070.88137.4270.0250.0250.0000.0000.0000.000
144B167SER00.0140.01440.913-0.001-0.0010.0000.0000.0000.000
145B168GLU-1-0.813-0.89544.493-0.017-0.0170.0000.0000.0000.000
146B169LEU0-0.002-0.00247.844-0.001-0.0010.0000.0000.0000.000
147B170HIS0-0.019-0.02050.2510.0020.0020.0000.0000.0000.000
148B171ILE0-0.0080.00754.260-0.001-0.0010.0000.0000.0000.000
149B172GLU-1-0.902-0.96357.584-0.014-0.0140.0000.0000.0000.000
150B173ASN0-0.004-0.00260.2970.0010.0010.0000.0000.0000.000
151B174LEU0-0.030-0.00958.7160.0000.0000.0000.0000.0000.000
152B175ASN00.0390.01062.7410.0010.0010.0000.0000.0000.000
153B176MET00.001-0.01963.9430.0000.0000.0000.0000.0000.000
154B177GLU-1-0.952-0.95865.861-0.005-0.0050.0000.0000.0000.000
155B178ALA0-0.008-0.00463.4850.0000.0000.0000.0000.0000.000
156B179ASP-1-0.738-0.84059.961-0.009-0.0090.0000.0000.0000.000
157B180PRO0-0.0060.01559.0810.0000.0000.0000.0000.0000.000
158B181GLY00.0200.00257.8990.0000.0000.0000.0000.0000.000
159B182GLN0-0.021-0.01552.5070.0000.0000.0000.0000.0000.000
160B183TYR00.003-0.00251.801-0.001-0.0010.0000.0000.0000.000
161B184ARG10.8240.88347.3310.0120.0120.0000.0000.0000.000
162B186ASN00.030-0.00443.3280.0030.0030.0000.0000.0000.000
163B187GLY00.0110.01140.345-0.002-0.0020.0000.0000.0000.000
164B188THR00.015-0.01139.1700.0020.0020.0000.0000.0000.000
165B189SER0-0.007-0.01133.545-0.002-0.0020.0000.0000.0000.000
166B190SER00.0330.01232.2670.0020.0020.0000.0000.0000.000
167B191LYS10.8740.94027.9020.0720.0720.0000.0000.0000.000
168B192GLY00.0460.03133.0660.0040.0040.0000.0000.0000.000
169B193SER0-0.004-0.01736.298-0.002-0.0020.0000.0000.0000.000
170B194ASP-1-0.808-0.88337.551-0.012-0.0120.0000.0000.0000.000
171B195GLN0-0.029-0.02439.6230.0010.0010.0000.0000.0000.000
172B196ALA00.004-0.00641.9990.0020.0020.0000.0000.0000.000
173B197ILE0-0.021-0.00744.106-0.001-0.0010.0000.0000.0000.000
174B198ILE0-0.048-0.02046.5070.0020.0020.0000.0000.0000.000
175B199THR0-0.033-0.02349.6170.0000.0000.0000.0000.0000.000
176B200LEU0-0.013-0.00853.0060.0000.0000.0000.0000.0000.000
177B201ARG10.9130.95155.788-0.003-0.0030.0000.0000.0000.000
178B202VAL00.0510.02558.7290.0000.0000.0000.0000.0000.000
179B203ARG10.7590.84258.8450.0010.0010.0000.0000.0000.000